From chemistry-request@ccl.net Sun Jun  5 20:32:28 2005
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From: "Jia, , joe" <032022046 :: fudan.edu.cn>
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Subject: W:how to solve this problem about gamess
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 *** ERROR *** IN -DAWRIT- ROUTINE ON NODE   0
 DAWRIT HAS REQUESTED A RECORD WITH LENGTH DIFFERENT THAN BEFORE - ABORT FORCED.
 DAF RECORD   322 NEW LENGTH =      2740 OLD LENGTH =      2760
 EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Tue May 31 19:12:52 2005
    26617208  WORDS OF DYNAMIC MEMORY USED
 STEP CPU TIME =    29.50 TOTAL CPU TIME =      667.3 (   11.1 MIN)
 TOTAL WALL CLOCK TIME=      676.6 SECONDS, CPU UTILIZATION IS  98.63%
 *** ERROR TERMINATION *** IN COMPUTE PROCESS     0

the error is -DAWRIT-- , which i have no idea about it. 

joe
032022046 :: fudan.edu.cn


From chemistry-request@ccl.net Mon Jun  6 08:29:06 2005
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Subject: Single point calculation in CRYSTAL03
Date: Mon, 6 Jun 2005 14:28:54 +0200
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From: "Ojwang, J.G.O." <j.g.o.ojwang:at:tue.nl>
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Dear all,
Is there anyone with an idea on how to perform single point calculation in CRYSTAL03 without geometry optimisation of the internal coordinates, something like freezing the atoms while expandinbg the lattice.

Regards,
Ojwang JGO



From chemistry-request@ccl.net Mon Jun  6 10:28:58 2005
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From: "Elie, , Cohen" <elie:at:drugdesign.com>
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Synergix Ltd. is pleased to announce the release of Molecular Conceptor v2.3

Molecular Conceptor is a computer-based course for teaching rational drug design and molecular modeling. The course contains more than 3000 slides, 1500 3D molecules and is the fruit of 7 years of intensive development.

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I invite you to get more details from our website:

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Elie Cohen
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Molecular Conceptor



From chemistry-request@ccl.net Mon Jun  6 05:36:57 2005
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Date: Mon, 6 Jun 2005 10:19:15 +0200
To: "Gustavo, , Mercier" <gamercier/at/yahoo.com>, chemistry/at/ccl.net
From: "Fco. Javier Modrego" <modrego/at/unizar.es>
Subject: Re: CCL:W:gOpenMol and Gamess MO plotting
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At 01:11 -0400 3/6/05, Gustavo, , Mercier wrote:
>Hi!
>
>I am interested in plotting MO's computed using GAMESS-US. I've 
>tried several programs with limited succes (molden, molekel, 
>orbdraw) and now I am trying gOpenMol.
>
>Looking at the manual etc I need to generate a cube file that will 
>be converted to the plt format read by gOpenMol using a plugin. 
>However, it is not clear to me how to generate the cube file using 
>GAMESS-US.

Look at the keyword PLTORB in the $CONTRL section of the Gamess' 
manual, then as stated in the gOpenMol pages, use Gamess2plt to 
convert a Gamess "cube" PUNCH file to a plt file. Otherwise if you 
can use a Mac , the program MacMolPlt is the easiest way of doing 
what you need.


I hope this can help you,

  Dr. F.J. Modrego
  Department of Inorganic Chemistry
  Facultad de Ciencias
  University of Zaragoza
  50009 ZARAGOZA
  SPAIN
  Tel <34>-976-762288
  Fax <34>-976-761187
  E-mail:  modrego/at/unizar.es


From chemistry-request@ccl.net Mon Jun  6 04:10:32 2005
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Date: Mon, 6 Jun 2005 14:30:47 +0800 (HKT)
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Dear all,

I found from the literature that a matrix will have all real
eigenvalues if it is pseudo-hermitian. For pseudo-hermitian, it means

\etta A \etta^{-1} = A^{daggar}

where \etta is a hermitian and invertible matrix and A is the matrix we
are interested in.

However, if given a matrix with complex eigenvalues, how can I make it
pseudo-hermitian with minimal changes to the matrix elements? Is there
any simple way to do it?
Thank you very much

Best regards,
Yam



From chemistry-request@ccl.net Mon Jun  6 06:52:31 2005
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Date: Mon, 06 Jun 2005 11:34:44 +0200
From: Karla Tersago <karla.tersago:at:ua.ac.be>
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Subject: conflict between energy and imaginary frequency
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Dear CCL'ers,

When I perform a geometry optimization, with frequency calculation of a 
certain molecule with Gaussian03, I have the following problem:
Cs symmetry: imaginary frequency of -20 cm-1, so this is transition 
state structure.
C1 symmetry: no imaginary frequencies, so it is a minimum on the 
potential energy surface. It's lowest frequency is 27 cm-1.
I checked the normal modes of both structures and the imaginary 
frequency of the Cs form and the lowest frequency of the C1 form 
correspond to the same normal mode.
The problem is that energy of the optimized structured shows that the Cs 
form has a lower energy (it is stabilized by 0.02 kcal/mol) than the C1 
form. 

How can it be that a transition state has a lower energy than a minimum? 

The calculations were done with B3LYP/6-311+G*
opt=verytight int=ultrafine freq 

As the data conflict, I thought it might be a problem with some 
thresholds, so I tried to set better thresholds with:
Iop(3/27=15) and Iop(3/29=15) 

I also tried iop(3/32=x) in combination with the above set options, but 
for x=3,4,5 the scf did not converged (even not if I put MaxCycle on 500). 

Does anybody have any suggestions on how I can solve this? 

Best regards,

Karla

-- 
-----------------------------------------------------------------------------
Karla Tersago
Structural Chemistry Group, Department of Chemistry
University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
E-mail: karla.tersago:at:ua.ac.be /Phone:+32(03)8202366/Fax:+32(03)8202310 
-----------------------------------------------------------------------------


--------------090007090500050901000702
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1">
  <title></title>
</head>
<body text="#000000" bgcolor="#ffffff">
<p class="MsoNormal">Dear CCL&#8217;ers,</p>
<p class="MsoNormal"><o:p></o:p>When I perform a geometry optimization,
with frequency
calculation of a certain molecule with Gaussian03, I have the following
problem:<br>
<o:p></o:p>Cs symmetry: imaginary frequency of -20 cm<sup>-1</sup>, so
this is transition state structure.<br>
C1 symmetry: no imaginary frequencies, so it is a minimum on
the potential energy surface. It&#8217;s lowest frequency is 27 cm<sup>-1</sup>.<br>
I checked the normal modes of both structures and the
imaginary frequency of the Cs form and the lowest frequency of the C1
form
correspond to the same normal mode.<br>
The problem is that energy of the optimized structured shows
that the Cs form has a lower energy (it is stabilized by 0.02 kcal/mol)
than
the C1 form.<o:p>&nbsp;</o:p></p>
<p class="MsoNormal">How can it be that a transition state has a lower
energy
than a minimum?<o:p>&nbsp;</o:p></p>
<p class="MsoNormal">The calculations were done with B3LYP/6-311+G*<br>
opt=verytight int=ultrafine freq<o:p>&nbsp;</o:p></p>
<p class="MsoNormal">As the data conflict, I thought it might be a
problem with
some thresholds, so I tried to set better thresholds with:<br>
Iop(3/27=15) and Iop(3/29=15)<o:p>&nbsp;</o:p></p>
<p class="MsoNormal">I also tried iop(3/32=x) in combination with the
above set
options, but for x=3,4,5 the scf did not converged (even not if I put
MaxCycle
on 500).<o:p>&nbsp;</o:p></p>
<p class="MsoNormal">Does anybody have any suggestions on how I can
solve this?<o:p>&nbsp;</o:p></p>
<p class="MsoNormal">Best regards,</p>
<p class="MsoNormal">Karla</p>
<pre class="moz-signature" cols="72">-- 
-----------------------------------------------------------------------------
Karla Tersago
Structural Chemistry Group, Department of Chemistry
University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:karla.tersago:at:ua.ac.be">karla.tersago:at:ua.ac.be</a> /Phone:+32(03)8202366/Fax:+32(03)8202310 
-----------------------------------------------------------------------------</pre>
</body>
</html>

--------------090007090500050901000702--



From chemistry-request@ccl.net Mon Jun  6 11:34:04 2005
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Subject: RE: Radical Dimerization 
Date: Mon, 6 Jun 2005 10:37:27 -0400
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Thread-Topic: Radical Dimerization 
Thread-Index: AcVpECjmrQ0WNMp6Qqa8wNN5RYvF+wBkIj7A
From: "Shobe, David" <dshobe :a: sud-chemieinc.com>
To: "may abdelghani" <may01dz :a: yahoo.fr>,
        "Wai-To Chan" <chan :a: curl.gkcl.yorku.ca>
Cc: "ccl" <chemistry :a: ccl.net>
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I reproduce May's original post:  (for textual analysis :-)
> Hello,CCLers
> I want to study theoretically the Radical Dimerization of some monomers; 
> I would like to know, in particularly, why some dimizations is not acceble 
> (we can not build the polymer from this monomers). My question is: what are 
> the properties (total energy, spin density, charge density  ), that I should
> calculate, in order to answer on this problem?  
> Best regard
> may abdelghani

'acceble' is missing some letters and could be either 'acceptable' or 'accessible'.  Assuming the 2nd interpretation, the idea would be that if the monomer doesn't dimerize, it doesn't polymerize because dimerization is the first step of polymerization.  

Perhaps there is some parameter from conceptual density functional theory that indicates the propensity for radical attack.  Of course you could also calculate activation energy for the process by calculating the transition state, e.g. for polyethylene:  CH3CH2. + CH2CH2 --> CH3CH2CH2CH2.

--David Shobe, Ph.D., M.L.S.
S|d-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a firewall.



-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request :a: ccl.net] On Behalf Of may abdelghani
Sent: Saturday, June 04, 2005 3:59 AM
To: Wai-To Chan
Cc: ccl
Subject: CCL:Radical Dimerization 

Hello,CCLers (Mr Wai-To Chan)
Thank you very much Dr Wai-To Chan, for your reply
(help) on my message (problem),
What is the difference between the tow
The problem in other world; what is the factors that difficult (or help) the polymer formation.

>     When you said 'dimerization is not *acceptable*'
> did you mean that
> dimerization is not desired for the purpose of the synthesis of a 
> polymer or did you mean you cannot build a polymer because the radical 
> monomers fail to dimerize?

What is the difference between the tow ? or what is the factors that difficult (or help) the polymer formation.
best regards
may abdelghani



	

	
		
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From chemistry-request@ccl.net Mon Jun  6 10:57:00 2005
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Date: Mon, 6 Jun 2005 22:19:21 +0800
From: "Ding Xunlei" <dxl :a: ustc.edu.cn>
Reply-To: dxl :a: ustc.edu.cn
To: "RubinMeana Paqeda" <rubenmp :a: correo.uniovi.es>,
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Dear #:

!!!!Google beowulf, you will get what you want.

    Thank you for your help!
 				
Ding Xunlei
2005-06-06
______________________________________________

======= 2013-10-29 17:27:00 You have written: =======

>
>Hello CCLers,
>We want to obtain information about building cluster of Linux. Where 
>can we  obtain it?
>Thank in advanced
>
>Rubin Meana Paqeda Ph.D. Student
>Laboratorio de Qummica Computacional. 
>Dpto de Qummica Fmsica y Analmtica. Facultad de Qummica. Universidad 
>de Oviedo. C/Julian Claverma 8, 332006  Oviedo, Principado de Asturias,
>Spain
>e-mail: rubenmp :a: correo.uniovi.es
>Tel. +34-985105016
>Fax  
>
>
>
>
>
>
>
>
>
>
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From chemistry-request@ccl.net Mon Jun  6 11:04:38 2005
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From: "Xavier ASSFELD" <Xavier.Assfeld -()- cbt.uhp-nancy.fr>
To: "Karla Tersago" <karla.tersago -()- ua.ac.be>, <chemistry -()- ccl.net>
Subject: RE: conflict between energy and imaginary frequency
Date: Mon, 6 Jun 2005 17:04:05 +0200
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Dear,

there are two possible explainations. The first one, as you mentioned is the
numerical noise due to the grid of integration. The cure is to use a
"better" grid! Is it possible?
The second possibility is intramolecular BSSE. Look at the work of Franck
Jensen Chem. Phys. Lett. 261 (1996) 633.
Yours.
                               ...Xav

Pr. Xavier Assfeld             Xavier.Assfeld -()- cbt.uhp-nancy.fr
Chimie et Biochimie theoriques T: (33) 3 83 68 43 82
Faculte des Sciences           F: (33) 3 83 68 43 71
54506 Vandoeuvre, France       http://www.lctn.uhp-nancy.fr

  -----Message d'origine-----
  De : Computational Chemistry List [mailto:chemistry-request -()- ccl.net]De la
part de Karla Tersago
  Envoye : lundi 6 juin 2005 11:35
  A : chemistry -()- ccl.net
  Objet : CCL:conflict between energy and imaginary frequency


  Dear CCL'ers,

  When I perform a geometry optimization, with frequency calculation of a
certain molecule with Gaussian03, I have the following problem:
  Cs symmetry: imaginary frequency of -20 cm-1, so this is transition state
structure.
  C1 symmetry: no imaginary frequencies, so it is a minimum on the potential
energy surface. It's lowest frequency is 27 cm-1.
  I checked the normal modes of both structures and the imaginary frequency
of the Cs form and the lowest frequency of the C1 form correspond to the
same normal mode.
  The problem is that energy of the optimized structured shows that the Cs
form has a lower energy (it is stabilized by 0.02 kcal/mol) than the C1
form.

  How can it be that a transition state has a lower energy than a minimum?

  The calculations were done with B3LYP/6-311+G*
  opt=verytight int=ultrafine freq

  As the data conflict, I thought it might be a problem with some
thresholds, so I tried to set better thresholds with:
  Iop(3/27=15) and Iop(3/29=15)

  I also tried iop(3/32=x) in combination with the above set options, but
for x=3,4,5 the scf did not converged (even not if I put MaxCycle on 500).

  Does anybody have any suggestions on how I can solve this?

  Best regards,

  Karla

--
----------------------------------------------------------------------------
-
Karla Tersago
Structural Chemistry Group, Department of Chemistry
University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
E-mail: karla.tersago -()- ua.ac.be /Phone:+32(03)8202366/Fax:+32(03)8202310
----------------------------------------------------------------------------
-

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	charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD><TITLE></TITLE>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Dus-ascii">
<META content=3D"MSHTML 6.00.2900.2627" name=3DGENERATOR></HEAD>
<BODY text=3D#000000 bgColor=3D#ffffff>
<DIV><SPAN class=3D451054614-06062005><FONT face=3DArial color=3D#0000ff =

size=3D2>Dear,</FONT></SPAN></DIV>
<DIV><SPAN class=3D451054614-06062005><FONT face=3DArial color=3D#0000ff =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D451054614-06062005><FONT face=3DArial color=3D#0000ff =
size=3D2>there=20
are two possible explainations. The first one, as you mentioned is the =
numerical=20
noise due to the grid of integration. The cure is to use a "better" =
grid! Is it=20
possible?</FONT></SPAN></DIV>
<DIV><SPAN class=3D451054614-06062005><FONT face=3DArial color=3D#0000ff =
size=3D2>The=20
second possibility is&nbsp;intramolecular BSSE. Look at the work =
of&nbsp;Franck=20
Jensen Chem. Phys. Lett. 261 (1996) 633.</FONT></SPAN></DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2><SPAN=20
class=3D451054614-06062005>Yours.</SPAN></FONT></DIV>
<P>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <FONT=20
size=3D2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ...Xav<BR><BR>Pr. Xavier=20
Assfeld&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;=20
Xavier.Assfeld -()- cbt.uhp-nancy.fr<BR>Chimie et Biochimie th&eacute;oriques =
T: (33) 3 83=20
68 43 82<BR>Facult&eacute; des=20
Sciences&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F: =
(33) 3=20
83 68 43 71<BR>54506 Vandoeuvre, =
France&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <A=20
href=3D"http://www.lctn.uhp-nancy.fr/"=20
target=3D_blank>http://www.lctn.uhp-nancy.fr</A></FONT> </P>
<BLOCKQUOTE dir=3Dltr=20
style=3D"PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px =
solid; MARGIN-RIGHT: 0px">
  <DIV class=3DOutlookMessageHeader dir=3Dltr align=3Dleft><FONT =
face=3DTahoma=20
  size=3D2>-----Message d'origine-----<BR><B>De&nbsp;:</B> Computational =
Chemistry=20
  List [mailto:chemistry-request -()- ccl.net]<B>De la part de</B> Karla=20
  Tersago<BR><B>Envoy&eacute;&nbsp;:</B> lundi 6 juin 2005 =
11:35<BR><B>&Agrave;&nbsp;:</B>=20
  chemistry -()- ccl.net<BR><B>Objet&nbsp;:</B> CCL:conflict between energy =
and=20
  imaginary frequency<BR><BR></FONT></DIV>
  <P class=3DMsoNormal>Dear CCL&#8217;ers,</P>
  <P class=3DMsoNormal><O:P></O:P>When I perform a geometry =
optimization, with=20
  frequency calculation of a certain molecule with Gaussian03, I have =
the=20
  following problem:<BR><O:P></O:P>Cs symmetry: imaginary frequency of =
-20=20
  cm<SUP>-1</SUP>, so this is transition state structure.<BR>C1 =
symmetry: no=20
  imaginary frequencies, so it is a minimum on the potential energy =
surface.=20
  It&#8217;s lowest frequency is 27 cm<SUP>-1</SUP>.<BR>I checked the =
normal modes of=20
  both structures and the imaginary frequency of the Cs form and the =
lowest=20
  frequency of the C1 form correspond to the same normal mode.<BR>The =
problem is=20
  that energy of the optimized structured shows that the Cs form has a =
lower=20
  energy (it is stabilized by 0.02 kcal/mol) than the C1=20
  form.<O:P>&nbsp;</O:P></P>
  <P class=3DMsoNormal>How can it be that a transition state has a lower =
energy=20
  than a minimum?<O:P>&nbsp;</O:P></P>
  <P class=3DMsoNormal>The calculations were done with=20
  B3LYP/6-311+G*<BR>opt=3Dverytight int=3Dultrafine =
freq<O:P>&nbsp;</O:P></P>
  <P class=3DMsoNormal>As the data conflict, I thought it might be a =
problem with=20
  some thresholds, so I tried to set better thresholds =
with:<BR>Iop(3/27=3D15) and=20
  Iop(3/29=3D15)<O:P>&nbsp;</O:P></P>
  <P class=3DMsoNormal>I also tried iop(3/32=3Dx) in combination with =
the above set=20
  options, but for x=3D3,4,5 the scf did not converged (even not if I =
put MaxCycle=20
  on 500).<O:P>&nbsp;</O:P></P>
  <P class=3DMsoNormal>Does anybody have any suggestions on how I can =
solve=20
  this?<O:P>&nbsp;</O:P></P>
  <P class=3DMsoNormal>Best regards,</P>
  <P class=3DMsoNormal>Karla</P><PRE class=3Dmoz-signature =
cols=3D"72">--=20
-------------------------------------------------------------------------=
----
Karla Tersago
Structural Chemistry Group, Department of Chemistry
University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
E-mail: <A class=3Dmoz-txt-link-abbreviated =
href=3D"mailto:karla.tersago -()- ua.ac.be">karla.tersago -()- ua.ac.be</A> =
/Phone:+32(03)8202366/Fax:+32(03)8202310=20
-------------------------------------------------------------------------=
----</PRE></BLOCKQUOTE></BODY></HTML>

------=_NextPart_000_0010_01C56AB9.BEC89E80--



From chemistry-request@ccl.net Mon Jun  6 13:07:46 2005
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Date: Mon,  6 Jun 2005 19:07:36 +0200
From: Stanislav.Ivan !=! unibas.ch
To: chemistry !=! ccl.net
Subject: Interatomic parameter tables
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Dear CCl'ers,
does anyone know some utility that is able to print out interatomic distance
tables (and table of angles, torsional angles) from pbd (zmt, xyz) structural
file ? Thank you very much.

Stan

--
Stanislav Ivan
Universitdt Basel
Departement Chemie
St.Johanns-Ring 19
4056 Basel
Switzerland

Tel.: (+41) (61) 267 11 44
Email: stanislav.ivan !=! unibas.ch

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From chemistry-request@ccl.net Mon Jun  6 18:23:51 2005
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Date: Mon, 06 Jun 2005 14:43:50 -0700
To: amber {} scripps.edu, CHEMISTRY {} ccl.net
From: Laurence Lavelle <lavelle {} mbi.ucla.edu>
Subject: Protein dynamics.
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In looking at the dynamical motion of a protein, is Amber (Cornell et al. 
(1994) force field) (Amber 99 parameters) considered a reasonably realistic 
protein force field (or, as good as or better than most) ?

In looking at the dynamical motion of a protein (for example using Amber), 
what are the pros and cons to doing Molecular Dynamics vs Langevin Dynamics 
vs Monte Carlo ?

{Some will say it depends on the details (distance dependent dielectric vs 
explicit solvent water molecules, no cutoffs vs with switched or shifted 
cutoffs, with or without periodic boundary conditions, etc.). However I am 
hoping (in addition to the above two questions) to get a general sense of 
how realistic MD, LD and MC are with respect to illustrating protein 
motion. By protein motion I mean a folded protein in a constant temperature 
simulation (for example with a distance dependent dielectric, no 
electrostatic cutoffs, no periodic boundaries) and comparing the protein 
dynamics at different temperatures.
To be explicit, I am not talking about protein folding or unfolding pathways.}

Thanks,
Laurence Lavelle




From chemistry-request@ccl.net Mon Jun  6 18:32:55 2005
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From: "Daniel A. Singleton" <singleton[at]mail.chem.tamu.edu>
Subject: CCL:conflict between energy and imaginary frequency
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Dear Karla and Xav,
      If the energies that Karla is talking about include 
zero point energy, then this is a common issue.  I have 
seen the potential energy + zpe for a transition structure 
exceed that of a close-by minimum at least a couple of 
dozen times (out of several thousand calculations).  The 
issue is that the zpe for the minimum has one extra 
contributing normal mode compared to the transition 
structure, and this adds to its zpe.  In reality, the zpe 
is being wrongly calculated by the harmonic approximation 
in these cases.  However, under any circumstances, one 
should not take too seriously a minimum that is in such an 
exceedingly shallow well.
      I don't see how BSSE can cause what was observed.  I 
suppose an integration grid issue might, in principle, 
though I've never ran into that with an ultrafine grid. 
 Finally, make sure all of the cartesian forces on the 
'optimzed' structures are small - in my experience for 
simple structures, about 1% of optimizations in reduntant 
internal coordinates lead to structures that are not 
really fully optimized, even with opt=verytight.
Dan Singleton


  Dear,
  
  there are two possible explainations. The first one, as
you mentioned is the
  numerical noise due to the grid of integration. The cure
is to use a
  "better" grid! Is it possible?
  The second possibility is intramolecular BSSE. Look at
the work of Franck
  Jensen Chem. Phys. Lett. 261 (1996) 633.
  Yours.
                                ...Xav
  
  Pr. Xavier Assfeld
             Xavier.Assfeld[at]cbt.uhp-nancy.fr
  Chimie et Biochimie theoriques T: (33) 3 83 68 43 82
Faculte des Sciences           F: (33) 3 83 68 43 71
  54506 Vandoeuvre, France
       http://www.lctn.uhp-nancy.fr
  
   -----Message d'origine-----
   De : Computational Chemistry List
[mailto:chemistry-request[at]ccl.net]De la
  part de Karla Tersago
   Envoye : lundi 6 juin 2005 11:35
   A : chemistry[at]ccl.net
   Objet : CCL:conflict between energy and imaginary
frequency
  
  
   Dear CCL'ers,
  
   When I perform a geometry optimization, with frequency
calculation of a
  certain molecule with Gaussian03, I have the following
problem:
   Cs symmetry: imaginary frequency of -20 cm-1, so this 
is
transition state
  structure.
   C1 symmetry: no imaginary frequencies, so it is a
minimum on the potential
  energy surface. It's lowest frequency is 27 cm-1.
   I checked the normal modes of both structures and the
imaginary frequency
  of the Cs form and the lowest frequency of the C1 form
correspond to the
  same normal mode.
   The problem is that energy of the optimized structured
shows that the Cs
  form has a lower energy (it is stabilized by 0.02
kcal/mol) than the C1
  form.
  
   How can it be that a transition state has a lower 
energy
than a minimum?
  
   The calculations were done with B3LYP/6-311+G*
   opt=verytight int=ultrafine freq
  
   As the data conflict, I thought it might be a problem
with some
  thresholds, so I tried to set better thresholds with:
   Iop(3/27=15) and Iop(3/29=15)
  
   I also tried iop(3/32=x) in combination with the above
set options, but
  for x=3,4,5 the scf did not converged (even not if I put
MaxCycle on 500).
  
   Does anybody have any suggestions on how I can solve
this?
  
   Best regards,
  
   Karla
  
  --
  ----------------------------------------------------------------------------
  -
  Karla Tersago
  Structural Chemistry Group, Department of Chemistry
  University of Antwerp, Universiteitsplein 1, B-2610
Antwerp, Belgium
  E-mail: karla.tersago[at]ua.ac.be
/Phone:+32(03)8202366/Fax:+32(03)8202310
  ----------------------------------------------------------------------------
  -


From chemistry-request@ccl.net Mon Jun  6 18:30:54 2005
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From: Brian Salter-Duke <b_duke_at_octa4.net.au>
To: chemistry_at_ccl.net
Subject: Re: CCL:W:gOpenMol and Gamess MO plotting
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On Mon, Jun 06, 2005 at 10:19:15AM +0200, Fco. Javier Modrego wrote:
> At 01:11 -0400 3/6/05, Gustavo, , Mercier wrote:
> >Hi!
> >
> >I am interested in plotting MO's computed using GAMESS-US. I've 
> >tried several programs with limited succes (molden, molekel, 
> >orbdraw) and now I am trying gOpenMol.
> >
> >Looking at the manual etc I need to generate a cube file that will 
> >be converted to the plt format read by gOpenMol using a plugin. 
> >However, it is not clear to me how to generate the cube file using 
> >GAMESS-US.
> 
> Look at the keyword PLTORB in the $CONTRL section of the Gamess' 
> manual, then as stated in the gOpenMol pages, use Gamess2plt to 
> convert a Gamess "cube" PUNCH file to a plt file. Otherwise if you 
> can use a Mac , the program MacMolPlt is the easiest way of doing 
> what you need.

I thought that PLTORB and cube were completely different. PLTORB gives a
2-dimensional grid but this is calculated in the pltorb graphics program
> from the data in the PUNCH file. A cube file contains the values in a
3-dimension grid that can indeed be translated into a plt file for
gOpenMol. I do not see how PLTORB in $CONTRL can give you anything that
can be used by gOpenMol. Am I confused? 
> 
> I hope this can help you,
> 
>  Dr. F.J. Modrego
>  Department of Inorganic Chemistry
>  Facultad de Ciencias
>  University of Zaragoza
>  50009 ZARAGOZA
>  SPAIN
>  Tel <34>-976-762288
>  Fax <34>-976-761187
>  E-mail:  modrego_at_unizar.es
> 
> 
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-- 
           Brian Salter-Duke (Brian Duke) b_duke_at_octa4.net.au  
        Post: 626 Melbourne Road, Spotswood, Vic 3015, Australia.
   Phone: 03-93992847. Web: http://members.iinet.net.au/~linden1/brian/
Honorary Researcher, Chemistry, Melbourne Univ, & Med. Chem., Monash Univ.